Genetic signatures of high-altitude adaptation and geographic distribution in Tibetan sheep

Jianbin Liu,Tingting Guo,Zengkui Lu,Xiaoping Sun,Xuezhi Ding,Chune Niu,Hao Zhang,Dingkao Renqing,Yaojing Yue,Xilan Xu,Fan Wang,Bohui Yang,Deqing Zhuoga,Yufeng Zeng,Chao Yuan

doi:10.1038/s41598-020-75428-4

Abstract

Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. However, the genetic mechanism regulating the multiple biological processes driving adaptive responses remains unclear. In this study, we applied a selective sweep analysis by combing 1% top values of Fst and ZHp on both altitude and geographic subpopulations (APS) in 636 indigenous Tibetan sheep breeds. Results show that 37 genes were identified within overlapped genomic regions regarding Fst significantly associated with APS. Out of the 37 genes, we found that 8, 3 and 6 genes at chromosomes (chr.) 13, 23 and 27, respectively, were identified in the genomic regions with 1% top values of ZHp. We further analyzed the INDEL variation of 6 genes at chr.27 (X chromosome) in APS together with corresponding orthologs of 6 genes in Capra, Pantholops, and Bos Taurus. We found that an INDEL was located within 5′UTR region of HAG1 gene. This INDEL of HAG1 was strongly associated with the variation of APS, which was further confirmed by qPCR. Sheep breeds carrying “C-INDEL” of HAG1 have significantly greater body weight, shear amount, corpuscular hemoglobin and globulin levels, but lower body height, than those carrying “CA-INDEL” of HAG1. We concluded that “C-INDEL” variation of HAG1 gene confers better hypoxia tolerance in the highlands of Tibetan and explains well geographic distributions in this population. These results contribute to our understanding of adaptive responses to altitude and geographic adaptation in Tibetan sheep populations and will help to guide future conservation programs for Tibetan sheep native to Qinghai-Tibetan Plateau.

Highlights

Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits
We sequenced 15 indigenous Tibetan sheep populations consisting of 636 individuals, originated from different geographic locations (Table 2), via high-resolution whole genomic sequences techniques (WGS)
To dissect the genomic heterozygosity levels and recombination events, we classified the populations into different altitude and geographic subpopulations (APS), including high altitude hypoxia (> 4500 m) vs. low altitude hypoxia (< 3500 m), and three different geographic locations, i.e., Qinghai, Gansu, and Tibetan (Table 1)

Summary

Introduction

Most sheep breeding programs designed for the tropics and sub-tropics have to take into account the impacts of environmental adaptive traits. The influence of climate change, i.e., cold stress on living organisms is exacerbated at the interface of extreme environments that typically occur in high altitude, plateaus and desert r egions[4] At such breeding programmes for livestock in these regions should include both adaptive and production t raits[5]. Tibetan sheep (Ovis aries) have the ability to adapt to a wide range of agro-ecological conditions, and represent an excellent model to gain new insights into genetic mechanisms underlying the adaptive response of livestock to extreme environments 6,7 This is helpful to develop appropriate breeding programs under various scenarios of future climate change. Tibetan sheep have lived on the Tibetan plateau for thousands of years; the process and consequences of adaptation to this extreme environment conditions have not yet been elucidated 8

Objectives

Methods

Results

Conclusion